GeneAtlas | GenAnnotator API

Get Genome informations

get

Get Genome informations

Query parameters

limitintegerOptional

pagination

Example: 10

namestringOptional

genome name

Example: Escherichia_coli_cft073

speciesstringOptional

species

Example: eColi

annotationbooleanOptional

is the genome annotated ?

Example: true

Responses

200

successful operation

get

/data/api/genome

GET /data/api/genome HTTP/1.1
Host: 127.0.0.1:8000
Accept: */*

200

successful operation

{
  "count": 6,
  "next": "http://127.0.0.1:8000/data/api/genome/limit=1&offset=2",
  "previous": "http://127.0.0.1:8000/data/api/genome/limit=1&offset=1",
  "results": [
    {
      "name": "Escherichia_coli_cft073",
      "species": "eColi",
      "header": "Chromosome dna:chromosome chromosome:ASM666v1:Chromosome:1:5528445:1 REF",
      "annotation": false,
      "sequence": "AGCTTTTCATTCTGA",
      "length": 5528445,
      "gc_content": 0.5044473518613253
    }
  ]
}

Create a new Genome

post

Create a new Genome

Body

namestringRequiredExample: Escherichia_coli_cft073

speciesstringOptionalExample: eColi

headerstringRequiredExample: Chromosome dna:chromosome chromosome:ASM666v1:Chromosome:1:5528445:1 REF

annotationbooleanOptionalExample: false

sequencestringRequiredExample: AGCTTTTCATTCTGA

Responses

200

successful operation

400

Invalid input

422

Validation exception

post

/data/api/genome

POST /data/api/genome HTTP/1.1
Host: 127.0.0.1:8000
Content-Type: application/json
Accept: */*
Content-Length: 184

{
  "name": "Escherichia_coli_cft073",
  "species": "eColi",
  "header": "Chromosome dna:chromosome chromosome:ASM666v1:Chromosome:1:5528445:1 REF",
  "annotation": false,
  "sequence": "AGCTTTTCATTCTGA"
}

{
  "name": "Escherichia_coli_cft073",
  "species": "eColi",
  "header": "Chromosome dna:chromosome chromosome:ASM666v1:Chromosome:1:5528445:1 REF",
  "annotation": false,
  "sequence": "AGCTTTTCATTCTGA",
  "length": 5528445,
  "gc_content": 0.5044473518613253
}

Get gene(s) information

get

Get gene(s) information. Without parameters return all the genes.

Query parameters

limitintegerOptional

pagination

Example: 10

namestringOptional

gene name

Example: ABG72671

genomestringOptional

genome

Example: Escherichia_coli_cft073

annotatedbooleanOptional

is the gene annotated ?

Example: true

motifstringOptional

filter by a motif

Example: %ATCG% / %ATCG / ATCG%

Responses

200

successful operation

400

Invalid input

422

Validation exception

get

/data/api/gene

GET /data/api/gene HTTP/1.1
Host: 127.0.0.1:8000
Accept: */*

{
  "count": 6,
  "next": "http://127.0.0.1:8000/data/api/gene/limit=1&offset=2",
  "previous": "http://127.0.0.1:8000/data/api/gene/limit=1&offset=1",
  "results": [
    {
      "name": "ABG72671",
      "genome": "Escherichia_coli_cft073",
      "start": 883887,
      "end": 885101,
      "header": "ABG72671 cds chromosome:ASM1330v1:Chromosome:883887:885101",
      "sequence": "ATGATCGATGCGGCATGCATG",
      "annotated": true,
      "length": 5528445,
      "gc_content": 0.5044473518613253
    }
  ]
}

Create a new gene

post

Create a new gene

Body

namestringRequiredExample: ABG72671

genomestringRequiredExample: Escherichia_coli_cft073

startintegerOptionalExample: 883887

endintegerOptionalExample: 885101

headerstringRequiredExample: ABG72671 cds chromosome:ASM1330v1:Chromosome:883887:885101

sequencestringRequiredExample: ATGATCGATGCGGCATGCATG

annotatedbooleanOptionalExample: true

Responses

200

successful operation

400

Invalid input

post

/data/api/gene

POST /data/api/gene HTTP/1.1
Host: 127.0.0.1:8000
Content-Type: application/json
Accept: */*
Content-Length: 204

{
  "name": "ABG72671",
  "genome": "Escherichia_coli_cft073",
  "start": 883887,
  "end": 885101,
  "header": "ABG72671 cds chromosome:ASM1330v1:Chromosome:883887:885101",
  "sequence": "ATGATCGATGCGGCATGCATG",
  "annotated": true
}

{
  "name": "ABG72671",
  "genome": "Escherichia_coli_cft073",
  "start": 883887,
  "end": 885101,
  "header": "ABG72671 cds chromosome:ASM1330v1:Chromosome:883887:885101",
  "sequence": "ATGATCGATGCGGCATGCATG",
  "annotated": true
}

Get information about peptide(s)

get

Get information about peptide(s). Without parameters return all the peptides.

Query parameters

limitintegerOptional

pagination

Example: 10

namestringOptional

peptide name

Example: ABG72671

genestringOptional

coding gene

Example: ABG72671

annotatedbooleanOptional

is the peptide annotated ?

Example: true

motifstringOptional

filter by a motif

Example: %ATCG% / %ATCG / ATCG%

Responses

200

successful operation

400

Invalid ID supplied

404

Order not found

get

/data/api/peptide

GET /data/api/peptide HTTP/1.1
Host: 127.0.0.1:8000
Accept: */*

{
  "count": 6,
  "next": "http://127.0.0.1:8000/data/api/peptide/limit=1&offset=2",
  "previous": "http://127.0.0.1:8000/data/api/peptide/limit=1&offset=1",
  "results": [
    {
      "name": "ABG68044",
      "header": "ABG68044 pep chromosome:ASM1330v1:Chromosome:336:2798",
      "sequence": "MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEK",
      "gene": "ABG68044",
      "length": 820
    }
  ]
}

Get information about a annotation

get

get information about a annotation

Authorizations

AuthorizationstringRequired

Bearer authentication header of the form Bearer <token>.

Query parameters

gene_instancestringOptional

The annotation of the gene to be searched for

Example: ABG72671

Responses

200

successful operation

400

Invalid ID supplied

404

Order not found

get

/data/api/annotation

GET /data/api/annotation HTTP/1.1
Host: 127.0.0.1:8000
Authorization: Bearer YOUR_SECRET_TOKEN
Accept: */*

{
  "gene": {
    "gene_instance": "AHA50631",
    "strand": -1,
    "gene": "b4705",
    "gene_biotype": "protein_coding",
    "transcript_biotype": "protein_coding",
    "gene_symbol": "mntS",
    "description": "Mn(2)-response protein, MntR-repressed",
    "is_current": true,
    "status": "AHA50631"
  },
  "peptide": {
    "peptide": "AHA50631",
    "transcript": "AHA50631",
    "annotation": "AHA50631"
  }
}

Update annotations

put

Update annotations. User must be identified and present one of the following roles annotator / validator

Authorizations

AuthorizationstringRequired

Bearer authentication header of the form Bearer <token>.

Path parameters

genestringRequired

Gene for which the annotation need to be updated

Example: AHA50631

Body

strandintegerOptionalExample: -1

genestringOptionalExample: b4705

gene_biotypestringOptionalExample: protein_coding

transcript_biotypestringOptionalExample: protein_coding

gene_symbolstringOptionalExample: mntS

descriptionstringOptionalExample: Mn(2)-response protein, MntR-repressed

is_currentbooleanOptionalExample: true

statusstringOptionalExample: AHA50631

transcriptstringOptionalExample: AHA50631

Responses

200

successful operation

400

Invalid ID supplied

404

Order not found

put

/data/api/annotation/{gene}

PUT /data/api/annotation/{gene} HTTP/1.1
Host: 127.0.0.1:8000
Authorization: Bearer YOUR_SECRET_TOKEN
Content-Type: application/json
Accept: */*
Content-Length: 236

{
  "strand": -1,
  "gene": "b4705",
  "gene_biotype": "protein_coding",
  "transcript_biotype": "protein_coding",
  "gene_symbol": "mntS",
  "description": "Mn(2)-response protein, MntR-repressed",
  "is_current": true,
  "status": "AHA50631",
  "transcript": "AHA50631"
}

{
  "gene_annotation": {
    "gene_instance": "AHA50631",
    "strand": -1,
    "gene": "b4705",
    "gene_biotype": "protein_coding",
    "transcript_biotype": "protein_coding",
    "gene_symbol": "mntS",
    "description": "Mn(2)-response protein, MntR-repressed",
    "is_current": true,
    "status": "AHA50631"
  },
  "peptide_annotation": {
    "peptide": "AHA50631",
    "transcript": "AHA50631",
    "annotation": "AHA50631"
  }
}

Get the status of a annotation

get

Get the status of a annotation

Authorizations

AuthorizationstringRequired

Bearer authentication header of the form Bearer <token>.

Query parameters

genestringOptional

the status of the annotation for the gene searched

Example: ABG68043

statusstringOptional

the status of annotation(s) searched

Example: RAW / ONGOING / PENDING / APPROVED / REJECTED

annotatorstringOptional

the annotator assigned to the annotations sought

Example: LeoooJr

limitintegerOptional

Paginate the result

Example: 10

Responses

200

successful operation

get

/data/api/status

GET /data/api/status HTTP/1.1
Host: 127.0.0.1:8000
Authorization: Bearer YOUR_SECRET_TOKEN
Accept: */*

200

successful operation

{
  "gene": "ABG68043",
  "status": "ONGOING",
  "created_at": "2025-01-16T09:24:11.268982Z",
  "updated_at": "2025-01-19T11:08:21.458418Z",
  "validated_at": null,
  "rejection_reason": null,
  "annotator": "leooojr"
}

Update annotation's status

put

Update annotation's status. User must be identified and present one of the following roles annotator / validator

Authorizations

AuthorizationstringRequired

Bearer authentication header of the form Bearer <token>.

Body

actionstringOptionalExample: setuser / approve / reject / submit

reasonstringOptional

if the action if rejected

Example: Gene symbol is not right

userstringOptional

the user to be set if action is setuser

Example: leooojr

geneone ofOptional

if action is setuser, can be done in batch of genes

stringOptionalExample: ABG68050

or

string[]OptionalExample: ABG68050

Responses

200

successful operation

put

/data/api/status

PUT /data/api/status HTTP/1.1
Host: 127.0.0.1:8000
Authorization: Bearer YOUR_SECRET_TOKEN
Content-Type: application/json
Accept: */*
Content-Length: 119

{
  "action": "setuser / approve / reject / submit",
  "reason": "Gene symbol is not right",
  "user": "leooojr",
  "gene": "ABG68050"
}

200

successful operation

{
  "status": {
    "ABG68050": true
  },
  "message": {
    "ABG68050": "user leooojr set for ABG68050"
  }
}

Get statistiques about GeneAtlas database / about a user

get

Get statistiques about GeneAtlas databases

Query parameters

userstringOptional

get stats about a user

Example: LeoooJr

Responses

default

successful operation

get

/data/api/stats

GET /data/api/stats HTTP/1.1
Host: 127.0.0.1:8000
Accept: */*

default

successful operation

{
  "annotations": 19,
  "ongoing": {
    "count": 8,
    "annotation": [
      "ABG68050..."
    ]
  },
  "pending": {
    "count": 1,
    "annotation": [
      "ABG68043..."
    ]
  },
  "approved": {
    "count": 10,
    "annotation": [
      "ABG68056..."
    ]
  }
}

Get information about asynchronous task

get

Get information about asynchronous task

Query parameters

keystringOptional

task's key

Example: 463e8a40-0a89-44c6-aaab-c904d03b0c7c

taskstringOptional

kind of task

Example: BLAST

userstringOptional

user who created the task

Example: leooojr

statestring · enumOptional

state of the task

Possible values:

Responses

200

successful operation

get

/data/api/tasks/

GET /data/api/tasks/ HTTP/1.1
Host: 127.0.0.1:8000
Accept: */*

200

successful operation

{
  "key": "463e8a40-0a89-44c6-aaab-c904d03b0c7c",
  "task": "BLAST",
  "user": "leooojr",
  "state": "COMPLETED",
  "error_message": null,
  "created_at": "2025-01-26T12:16:53.564813Z",
  "updated_at": "2025-01-26T12:16:53.564824Z"
}

get information and result from a Blast task

get

get information and result from a Blast task

Authorizations

AuthorizationstringRequired

Bearer authentication header of the form Bearer <token>.

Query parameters

keystringRequired

key of the Blast task

Example: 0b3b8cab-02ef-48a1-8373-31cf12532f50

Responses

200

successful operation

get

/data/api/blast/

GET /data/api/blast/?key=0b3b8cab-02ef-48a1-8373-31cf12532f50 HTTP/1.1
Host: 127.0.0.1:8000
Authorization: Bearer YOUR_SECRET_TOKEN
Accept: */*

200

successful operation

{
  "task": "0b3b8cab-02ef-48a1-8373-31cf12532f50",
  "state": "COMPLETED",
  "user": "leooojr",
  "params": {
    "sequence": "ATGAAACGCATTAGCACCACCATTACCACCACCATCACCACCACCATCACCATTACCATTACCACAGGTAACGGTGCGGGCTGA",
    "program": "blastn",
    "database": "nt",
    "evalue": 0.001
  },
  "result": {}
}

execute a Blast

post

execute a Blast

Authorizations

AuthorizationstringRequired

Bearer authentication header of the form Bearer <token>.

Body

genestringOptional

gene to be blasted

Example: AAG54301

Responses

200

successful operation

post

/data/api/blast/

POST /data/api/blast/ HTTP/1.1
Host: 127.0.0.1:8000
Authorization: Bearer YOUR_SECRET_TOKEN
Content-Type: application/json
Accept: */*
Content-Length: 19

{
  "gene": "AAG54301"
}

200

successful operation

{
  "message": "BLAST job 0b3b8cab-02ef-48a1-8373-31cf12532f50 submitted."
}

hashtagGet Genome informations

hashtagCreate a new Genome

hashtagGet gene(s) information

hashtagCreate a new gene

hashtagGet information about peptide(s)

hashtagGet information about a annotation

hashtagUpdate annotations

hashtagGet the status of a annotation

hashtagUpdate annotation's status

hashtagGet statistiques about GeneAtlas database / about a user

hashtagGet information about asynchronous task

hashtagget information and result from a Blast task

hashtagexecute a Blast

Get Genome informations

Create a new Genome

Get gene(s) information

Create a new gene

Get information about peptide(s)

Get information about a annotation

Update annotations

Get the status of a annotation

Update annotation's status

Get statistiques about GeneAtlas database / about a user

Get information about asynchronous task

get information and result from a Blast task

execute a Blast